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Re: [ccp4bb] real-space vs. reciprocal space refinement |
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CCP4bb navigationCCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999Subject: Re: real-space vs. reciprocal space refinement From: Anastassis Perrakis a {- dot -} perrakis {- at -} NKI {- dot -} NL Date: 2007-08-10 On 10 Aug 2007, at 18:59, Pavel Afonine wrote: > Hi Mike, > > the best is to do both in a loop: > > for cycle in cycles: > - do real space refinement; > - do reciprocal space refinement Well - thats what we all do - right ? The real space refinement can be done either with the tools from Chapman at al, or interactively by the user or by (here I go again ... ) ARP/wARP or Resolve etc etc. In all cases we fit the model to the map ... only the tools differ. Although I would be tempted to suggest some general reading to Mike S@Gmail.com [1] (there is one copy of Blundell and Johnson available at Amazon for 1239.64$, quite a bargain) the most simple minded way to think of it is that in real space you fit a piece of model to a piece of density locally. In reciprocal space the data from the entire molecular model is fitted to the entire diffraction dataset at the same time. The argument about phases I think you know it, so I will not diatribe on this. ;-) Also, there are no more than 2-3 MAD experimental phase-sets out there (all in very high resolution) that can claim that the phases derived from them are as accurate as the phases from the refined model. Thus even if you let aside all of the rest of the theory, the phases we 'measure' these days are not that good. Also, usually we think of 'excellent' phases that come from density modification. Thats already modeling ... Finally, I think the vast majority of structures are still from molecular replacement, and thus you don't have good phases by definition. A. [1] Why don't people subscribe to ccp4 from their real institute email addresses ? PS Is nobody reading Nature these days or no-one likes a good argument about crystallographic models any more in this bb ? > > Have a look at this very nice paper: > > Acta Cryst. (1999). D55, 835-845 Critical initial real-space > refinement in the structure determination of arginine kinase > G. Zhou, T. Somasundaram, E. Blanc, Z. Chen and M. S. Chapman > > and other "real space refinement" related papers by M. S. Chapman > et al. > > Pavel. > > Mike S wrote: >> Dear CCP4 experts, >> >> Recently, I was debating a colleague on the pros/cons of >> refinement done in reciprocal space compared to refinement in real >> space. >> I always thought reciprocal space refinement was preferable since >> measured amplitudes will be more accurate than calculated phases >> (unless good experimental phases are available). My colleague >> argued that with sigmaA and maximum-likelihood methods, calculated >> phases are much "better" than they were in the past and the two >> refinement techniques are equivalent in terms of robustness. He >> said the reason most software hasn't switched entirely to real- >> space refinement is due to computational issues. >> >> Please help enlighten me. All comments/diatribes welcome. >> >> Thanks, >> Mike CCP4bb navigationCCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999 |
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